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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ), 'gf_id' => 'HOM05D001117', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001117' ), 'data_identifier' => 'HOM05D001117', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001117', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '550', 'num_species' => '94' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22290' => 'bna', 'A01p33090' => 'bna', 'A02p10270' => 'bna', 'A03p42060' => 'bna', 'A05p27570' => 'bna', 'A10p11700' => 'bna', 'Aa31LG3G10400' => 'aar', 'Aa31LG5G10190' => 'aar', 'Aa31LG8G7850' => 'aar', 'Aa31LG8G8450' => 'aar', 'Aa31LG9G2180' => 'aar', 'Actinidia05154' => 'ach', 'Actinidia05560' => 'ach', 'Actinidia09934' => 'ach', 'Actinidia12477' => 'ach', 'Actinidia30497' => 'ach', 'Actinidia30506' => 'ach', 'Actinidia39294' => 'ach', 'Ah.04g165300' => 'amhyb', 'Ah.06g183390' => 'amhyb', 'Ah.08g217770' => 'amhyb', 'Ah.09g236270' => 'amhyb', 'Ah.09g236520' => 'amhyb', 'Ah.14g088250' => 'amhyb', 'Ah.14g088260' => 'amhyb', 'Ah.14g088280' => 'amhyb', 'Ah.14g088290' => 'amhyb', 'Ah.14g088310' => 'amhyb', 'Ah.14g088320' => 'amhyb', 'Ah.14g088330' => 'amhyb', 'Ah.14g088770' => 'amhyb', 'Ah.15g094370' => 'amhyb', 'AL3G35090' => 'aly', 'AL3G36050' => 'aly', 'AL3G36070' => 'aly', 'AL7G25510' => 'aly', 'AL7G40380' => 'aly', 'AL8G29820' => 'aly', 'Aqoxy1G03739' => 'aox', 'Aqoxy4G02249' => 'aox', 'Aqoxy7G02853' => 'aox', 'Aqoxy7G03431' => 'aox', 'arahy.Tifrunner.gnm1.ann1.7CSR8W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7LA68K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HRDR92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K5EF2U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KBYK8P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PDLP37' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QUP41J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RN4BKJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RYFJ47' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UHV0SM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5JHRV' => 'arhy', 'AT3G21150' => 'ath', 'AT3G21890' => 'ath', 'AT4G15248' => 'ath', 'AT4G27310' => 'ath', 'AT5G54470' => 'ath', 'ATR1132G033' => 'atr', 'Atru.chr1.2719' => 'acertr', 'Atru.chr2.2943' => 'acertr', 'Atru.chr6.3098' => 'acertr', 'Atru.chr6.3138' => 'acertr', 'AUR62001354' => 'cqu', 'AUR62025650' => 'cqu', 'AUR62041163' => 'cqu', 'BcaB03g12531' => 'bca', 'BcaB04g19145' => 'bca', 'BcaB04g20553' => 'bca', 'BcaB05g22135' => 'bca', 'BcaB06g26185' => 'bca', 'BcaB06g26291' => 'bca', 'BcaB08g35802' => 'bca', 'BcaB08g35803' => 'bca', 'BcaC01g03524' => 'bca', 'BcaC03g14311' => 'bca', 'BcaC04g20335' => 'bca', 'BcaC05g28119' => 'bca', 'BcaC05g28254' => 'bca', 'BcaC06g32700' => 'bca', 'BcaC07g38278' => 'bca', 'BcaC09g49131' => 'bca', 'BcaC09g49132' => 'bca', 'BcaC09g50207' => 'bca', 'BcaC09g50586' => 'bca', 'BcaNung00293' => 'bca', 'BcaNung03042' => 'bca', 'BcaNung03044' => 'bca', 'BolC1t02290H' => 'bol', 'BolC1t02717H' => 'bol', 'BolC1t04187H' => 'bol', 'BolC2t07799H' => 'bol', 'BolC3t17433H' => 'bol', 'BolC5t32888H' => 'bol', 'BolC5t32986H' => 'bol', 'BolC7t46020H' => 'bol', 'BolC9t57353H' => 'bol', 'BraA01t01798Z' => 'bra', 'BraA01t02145Z' => 'bra', 'BraA01t03432Z' => 'bra', 'BraA02t06096Z' => 'bra', 'BraA03t13360Z' => 'bra', 'BraA05t21646Z' => 'bra', 'BraA10t43267Z' => 'bra', 'C01p27830' => 'bna', 'C01p42320' => 'bna', 'C02p17010' => 'bna', 'C03p51480' => 'bna', 'C05p41490' => 'bna', 'C05p42670' => 'bna', 'C09p44790' => 'bna', 'CAN.G1110.35' => 'can', 'CAN.G308.10' => 'can', 'CAN.G424.41' => 'can', 'CAN.G640.14' => 'can', 'CAN.G80.16' => 'can', 'CAN.G921.1' => 'can', 'CANSAT01G2657' => 'cansat', 'CANSAT11G1364' => 'cansat', 'CANSAT56G0737' => 'cansat', 'CANSAT64G1155' => 'cansat', 'CARHR097010' => 'chi', 'CARHR097850' => 'chi', 'CARHR221970' => 'chi', 'CARHR234960' => 'chi', 'CARHR267730' => 'chi', 'Carub.0003s2105' => 'cru', 'Carub.0003s2108' => 'cru', 'Carub.0003s2196' => 'cru', 'Carub.0007s1357' => 'cru', 'Carub.0007s2670' => 'cru', 'Carub.0008s1476' => 'cru', 'Ca_01555_v3' => 'car', 'Ca_20503_v3' => 'car', 'Cc02_g12170' => 'ccan', 'Cc05_g05180' => 'ccan', 'Cc05_g05670' => 'ccan', 'Cc05_g12830' => 'ccan', 'CDE02G4415' => 'cde', 'CDE05G1941' => 'cde', 'CDE05G3411' => 'cde', 'CDE11G0783' => 'cde', 'Cfa000309' => 'cfa', 'Cfa002141' => 'cfa', 'Cfa014442' => 'cfa', 'Cfa014492' => 'cfa', 'Cfa020485' => 'cfa', 'Ciclev10009213m.g' => 'ccl', 'Ciclev10016798m.g' => 'ccl', 'Ciclev10017183m.g' => 'ccl', 'Ciclev10026364m.g' => 'ccl', 'CiPaw.01G090100' => 'cil', 'CiPaw.03G163400' => 'cil', 'CiPaw.03G166500' => 'cil', 'CiPaw.04G118200' => 'cil', 'CiPaw.04G121200' => 'cil', 'CiPaw.09G156200' => 'cil', 'CiPaw.10G115500' => 'cil', 'CiPaw.11G179100' => 'cil', 'ClCG01G022380' => 'cla', 'ClCG02G001760' => 'cla', 'ClCG02G008410' => 'cla', 'ClCG03G005420' => 'cla', 'ClCG05G015130' => 'cla', 'COL.COLO4_09503' => 'col', 'COL.COLO4_12999' => 'col', 'COL.COLO4_13055' => 'col', 'COL.COLO4_31183' => 'col', 'COL.COLO4_31639' => 'col', 'Cpa.g.c31349' => 'cpa', 'Cpa.g.sc34.54' => 'cpa', 'Cpa.g.sc8.240' => 'cpa', 'Cre06.g278200' => 'cre', 'CsaV3_2G035230' => 'csa', 'CsaV3_3G044220' => 'csa', 'CsaV3_6G049560' => 'csa', 'CsaV3_7G003780' => 'csa', 'CSS0013458' => 'camsi', 'CSS0027760' => 'camsi', 'CSS0042826' => 'camsi', 'CSS0045354' => 'camsi', 'CSS0046446' => 'camsi', 'CSS0048976' => 'camsi', 'DCAR_009704' => 'dca', 'DCAR_019210' => 'dca', 'DCAR_019775' => 'dca', 'DCAR_021190' => 'dca', 'DCAR_021204' => 'dca', 'Dinv02569' => 'din', 'Dinv12207' => 'din', 'Dinv13857' => 'din', 'Dinv18533' => 'din', 'Dinv20347' => 'din', 'Dinv22347' => 'din', 'Duzib052G1118' => 'dzi', 'Duzib132G1217' => 'dzi', 'Duzib160G0071' => 'dzi', 'Duzib160G0287' => 'dzi', 'Duzib192G0536' => 'dzi', 'Duzib192G0840' => 'dzi', 'Duzib213G0543' => 'dzi', 'Duzib235G1374' => 'dzi', 'Duzib248G0669' => 'dzi', 'Duzib248G0946' => 'dzi', 'Duzib268G1363' => 'dzi', 'ECA233G2745' => 'eca', 'ECA240G0030' => 'eca', 'ECA246G2042' => 'eca', 'EL10Ac4g08037' => 'bvu', 'EL10Ac7g18174' => 'bvu', 'EL10Ac8g19983' => 'bvu', 'Eucgr.E03673' => 'egr', 'Eucgr.F01063' => 'egr', 'Eucgr.F04023' => 'egr', 'Eucgr.K00864' => 'egr', 'FAN02G0150' => 'fan', 'FAN02G0164' => 'fan', 'FAN02G4522' => 'fan', 'FAN05G3136' => 'fan', 'FAN05G3317' => 'fan', 'FAN09G0344' => 'fan', 'FAN09G1618' => 'fan', 'FAN09G3929' => 'fan', 'FAN11G0347' => 'fan', 'FAN11G2630' => 'fan', 'FAN14G1056' => 'fan', 'FAN14G5585' => 'fan', 'FAN16G0114' => 'fan', 'FAN16G2363' => 'fan', 'FAN21G0029' => 'fan', 'FAN21G1510' => 'fan', 'FAN25G1248' => 'fan', 'FAN25G2345' => 'fan', 'FvH4_3g03640' => 'fve', 'FvH4_3g21230' => 'fve', 'FvH4_6g37140' => 'fve', 'FvH4_6g43580' => 'fve', 'FvH4_6g44270' => 'fve', 'Glyma.06G255300' => 'gma', 'Glyma.06G300900' => 'gma', 'Glyma.07G020400' => 'gma', 'Glyma.08G221600' => 'gma', 'Glyma.09G225450' => 'gma', 'Glyma.12G103800' => 'gma', 'Glyma.12G196200' => 'gma', 'Glyma.12G198400' => 'gma', 'Glyma.13G248000' => 'gma', 'Glyma.13G303700' => 'gma', 'Glyma.13G306300' => 'gma', 'Glyma.15G065900' => 'gma', 'Gohir.A01G070100' => 'ghi', 'Gohir.A03G162000' => 'ghi', 'Gohir.A03G163300' => 'ghi', 'Gohir.A04G024900' => 'ghi', 'Gohir.A04G107400' => 'ghi', 'Gohir.A06G130300' => 'ghi', 'Gohir.A12G134900' => 'ghi', 'Gohir.A12G135650' => 'ghi', 'Gohir.A13G058000' => 'ghi', 'Gohir.D01G057300' => 'ghi', 'Gohir.D02G185100' => 'ghi', 'Gohir.D02G186700' => 'ghi', 'Gohir.D04G147300' => 'ghi', 'Gohir.D05G362500' => 'ghi', 'Gohir.D06G127050' => 'ghi', 'Gohir.D12G138600' => 'ghi', 'Gohir.D13G064000' => 'ghi', 'Gorai.002G077700' => 'gra', 'Gorai.005G207500' => 'gra', 'Gorai.005G209000' => 'gra', 'Gorai.008G150000' => 'gra', 'Gorai.009G430000' => 'gra', 'Gorai.010G148100' => 'gra', 'Gorai.012G133300' => 'gra', 'Gorai.013G072700' => 'gra', 'GSVIVG01000440001' => 'vvi', 'GSVIVG01014471001' => 'vvi', 'GSVIVG01037173001' => 'vvi', 'HanXRQChr03g0076131' => 'han', 'HanXRQChr10g0297441' => 'han', 'HanXRQChr13g0407541' => 'han', 'HanXRQChr15g0479521' => 'han', 'HanXRQChr17g0543111' => 'han', 'HanXRQChr17g0552841' => 'han', 'Haze_06616' => 'cav', 'Haze_09554' => 'cav', 'Haze_12903' => 'cav', 'Haze_13025' => 'cav', 'Haze_16285' => 'cav', 'Haze_16287' => 'cav', 'Hma1.2p1_0517F.1_g170690' => 'hma', 'Hma1.2p1_0613F.1_g189230' => 'hma', 'HPP92_010077' => 'vpl', 'HPP92_014085' => 'vpl', 'Hund08058' => 'sun', 'Lalb_Chr01g0005511' => 'lal', 'Lalb_Chr01g0006341' => 'lal', 'Lalb_Chr01g0017121' => 'lal', 'Lalb_Chr03g0029001' => 'lal', 'Lalb_Chr03g0030341' => 'lal', 'Lalb_Chr14g0366501' => 'lal', 'Lalb_Chr15g0080031' => 'lal', 'Lalb_Chr19g0134571' => 'lal', 'Lalb_Chr20g0122441' => 'lal', 'Lalb_Chr22g0349601' => 'lal', 'Lalb_Chr22g0356261' => 'lal', 'Lj1P856T30' => 'lonja', 'Lj3g0003827' => 'lja', 'Lj3g0010117' => 'lja', 'Lj3g0018576' => 'lja', 'Lj3g0026940' => 'lja', 'Lj6g0006365' => 'lja', 'Lj8A119T45' => 'lonja', 'Lsat_1_v5_gn_0_5501' => 'lsa', 'Lsat_1_v5_gn_1_39541' => 'lsa', 'Lsat_1_v5_gn_3_41740' => 'lsa', 'Lsat_1_v5_gn_4_69761' => 'lsa', 'Lsat_1_v5_gn_8_131201' => 'lsa', 'Manes.03G117900' => 'mes', 'Manes.12G078100' => 'mes', 'Manes.12G079100' => 'mes', 'Manes.13G073800' => 'mes', 'Manes.13G082024' => 'mes', 'Manes.15G081202' => 'mes', 'Manes.16G019163' => 'mes', 'Manes.17G032600' => 'mes', 'Mapoly0049s0030' => 'mpo', 'Mapoly0061s0119' => 'mpo', 'MBI02_g03607_MAGBIO' => 'mbi', 'MBI02_g35707_MAGBIO' => 'mbi', 'MBI13_g34050_MAGBIO' => 'mbi', 'MBI16_g05841_MAGBIO' => 'mbi', 'MBI18_g30580_MAGBIO' => 'mbi', 'MBI18_g36121_MAGBIO' => 'mbi', 'MD09G1099500' => 'mdo', 'MD09G1104600' => 'mdo', 'MD17G1092200' => 'mdo', 'Medtr2g011450' => 'mtr', 'Medtr2g089310' => 'mtr', 'Medtr4g008050' => 'mtr', 'Medtr4g046640' => 'mtr', 'MELO3C002548.2' => 'cme', 'MELO3C007337.2' => 'cme', 'MELO3C018174.2' => 'cme', 'MELO3C018801.2' => 'cme', 'MELO3C019231.2' => 'cme', 'Migut.I01186' => 'egut', 'Migut.M00372' => 'egut', 'Migut.M00392' => 'egut', 'Migut.M01231' => 'egut', 'Migut.M01851' => 'egut', 'MSTRG.10885' => 'ama', 'MSTRG.11588' => 'ama', 'MSTRG.12295' => 'ama', 'MSTRG.14167' => 'ama', 'MSTRG.15188' => 'ama', 'MSTRG.7274' => 'ama', 'Nitab4.5_0000207g0320' => 'nta', 'Nitab4.5_0000631g0020' => 'nta', 'Nitab4.5_0000649g0230' => 'nta', 'Nitab4.5_0001320g0010' => 'nta', 'Nitab4.5_0001680g0030' => 'nta', 'Nitab4.5_0001691g0210' => 'nta', 'Nitab4.5_0002354g0010' => 'nta', 'Nitab4.5_0002750g0110' => 'nta', 'Nitab4.5_0002949g0020' => 'nta', 'Nitab4.5_0003757g0010' => 'nta', 'Nitab4.5_0004360g0050' => 'nta', 'Nitab4.5_0004625g0020' => 'nta', 'Nitab4.5_0005620g0060' => 'nta', 'Nitab4.5_0006975g0040' => 'nta', 'Nn1g03814' => 'nnu', 'Nn1g06843' => 'nnu', 'Nn8g40727' => 'nnu', 'Oeu001812.1' => 'oeu', 'Oeu006773.1' => 'oeu', 'Oeu008402.1' => 'oeu', 'Oeu021578.1' => 'oeu', 'Oeu031650.1' => 'oeu', 'Oeu034260.1' => 'oeu', 'Oeu041953.1' => 'oeu', 'Oeu044523.1' => 'oeu', 'Oeu045546.1' => 'oeu', 'Oeu055693.1' => 'oeu', 'Os02g0176000' => 'osa', 'Os06g0661200' => 'osa', 'Os08g0178800' => 'osa', 'Peaxi162Scf00007g01730' => 'pax', 'Peaxi162Scf00007g10129' => 'pax', 'Peaxi162Scf00257g10112' => 'pax', 'Peaxi162Scf00555g00028' => 'pax', 'PGR083G2619' => 'pgr', 'PGR102G1110' => 'pgr', 'PGR142G1034' => 'pgr', 'PGSC0003DMG400013178' => 'stu', 'PGSC0003DMG400013753' => 'stu', 'PGSC0003DMG400022345' => 'stu', 'PGSC0003DMG400025024' => 'stu', 'PGSC0003DMG400026169' => 'stu', 'PGSC0003DMG400026181' => 'stu', 'PGSC0003DMG400026515' => 'stu', 'Phvul.005G110600' => 'pvu', 'Phvul.005G113200' => 'pvu', 'Phvul.006G193800' => 'pvu', 'Phvul.008G254400' => 'pvu', 'Phvul.011G106300' => 'pvu', 'Phvul.011G108800' => 'pvu', 'Phvul.011G149800' => 'pvu', 'Potri.001G414700' => 'ptr', 'Potri.004G026900' => 'ptr', 'Potri.004G027000' => 'ptr', 'Potri.004G027100' => 'ptr', 'Potri.007G121100' => 'ptr', 'Potri.008G007000' => 'ptr', 'Potri.010G251800' => 'ptr', 'Potri.011G039700' => 'ptr', 'Potri.011G125400' => 'ptr', 'Potri.013G150500' => 'ptr', 'Potri.017G039400' => 'ptr', 'Pp3c11_6300' => 'ppa', 'Pp3c1_6980' => 'ppa', 'Pp3c2_30120' => 'ppa', 'Pp3c7_25550' => 'ppa', 'Prupe.3G020100' => 'ppe', 'Prupe.3G221100' => 'ppe', 'Prupe.3G226900' => 'ppe', 'Prupe.4G033600' => 'ppe', 'Prupe.4G192700' => 'ppe', 'Psat1g209600' => 'psa', 'Psat5g267200' => 'psa', 'Psat7g260760' => 'psa', 'PSO063G7143' => 'pso', 'PSO170G5160' => 'pso', 'PSO541G1682' => 'pso', 'PSO675G8739' => 'pso', 'QL05p080483' => 'qlo', 'QL05p083841' => 'qlo', 'QL08p017105' => 'qlo', 'QL08p033897' => 'qlo', 'QL08p035199' => 'qlo', 'QL08p035981' => 'qlo', 'RcHm_v2.0_Chr2g0149701' => 'rch', 'RcHm_v2.0_Chr2g0160161' => 'rch', 'RcHm_v2.0_Chr2g0161131' => 'rch', 'RcHm_v2.0_Chr5g0005681' => 'rch', 'RcHm_v2.0_Chr5g0036301' => 'rch', 'Rhsim04G0056900' => 'rsi', 'Rhsim04G0058600' => 'rsi', 'Rhsim06G0154100' => 'rsi', 'Rhsim06G0157700' => 'rsi', 'Rhsim06G0191700' => 'rsi', 'RhsimUnG0197900' => 'rsi', 'Sabra04G0015400' => 'sbr', 'Sabra07G0098100' => 'sbr', 'Sabra08G0003800' => 'sbr', 'Sabra10G0195900' => 'sbr', 'Sabra11G0112200' => 'sbr', 'Sabra13G0121000' => 'sbr', 'Sabra16G0272100' => 'sbr', 'Sabra16G0277100' => 'sbr', 'Sabra19G0120300' => 'sbr', 'Sabra19G0133600' => 'sbr', 'SalBow1G0303' => 'sbo', 'SalBow1G1129' => 'sbo', 'SalBow6G1297' => 'sbo', 'SalBow8G1985' => 'sbo', 'Sc12g0002400' => 'sci', 'Sc12g0002580' => 'sci', 'Sc12g0011110' => 'sci', 'Sc21g0002060' => 'sci', 'Sed0001274' => 'sed', 'Sed0001811' => 'sed', 'Sed0008702' => 'sed', 'Sed0009185' => 'sed', 'Sed0014421' => 'sed', 'Sed0025411' => 'sed', 'SEGI_11560' => 'sgi', 'SGA_v2.0_scaffold114G31995' => 'sas', 'SGA_v2.0_scaffold122G33279' => 'sas', 'SGA_v2.0_scaffold34G13898' => 'sas', 'SGA_v2.0_scaffold49G18320' => 'sas', 'SGA_v2.0_scaffold70G23437' => 'sas', 'SGA_v2.0_scaffold71G24000' => 'sas', 'SGA_v2.0_scaffold73G24330' => 'sas', 'SMO133G0012' => 'smo', 'Solyc02g079430.4' => 'sly', 'Solyc06g063280.1' => 'sly', 'Solyc07g052620.1' => 'sly', 'Solyc07g053140.3' => 'sly', 'Solyc12g005660.2' => 'sly', 'Solyc12g005750.1' => 'sly', 'Sopen02g024230' => 'spe', 'Sopen06g022740' => 'spe', 'Sopen07g026230' => 'spe', 'Sopen07g026690' => 'spe', 'Sopen10g002670' => 'spe', 'Sopen12g001590' => 'spe', 'Sp3g19110' => 'spa', 'Sp3g19860' => 'spa', 'Sp6g16440' => 'spa', 'Sp7g13460' => 'spa', 'Sp7g25230' => 'spa', 'TAR624G0032' => 'tar', 'TAR625G0819' => 'tar', 'TAR626G0811' => 'tar', 'TAR626G1563' => 'tar', 'TAR627G0659' => 'tar', 'TAR636G2388' => 'tar', 'THA.LOC104799898' => 'tha', 'THA.LOC104809280' => 'tha', 'THA.LOC104816867' => 'tha', 'THA.LOC104821750' => 'tha', 'Thecc.02G162800' => 'tca', 'Thecc.02G166700' => 'tca', 'Thecc.06G060100' => 'tca', 'Thecc.06G202800' => 'tca', 'Thecc.07G068500' => 'tca', 'Thhalv10014573m.g' => 'esa', 'Thhalv10021479m.g' => 'esa', 'Thhalv10021966m.g' => 'esa', 'Thhalv10026046m.g' => 'esa', 'TPR.G15694' => 'tpr', 'TPR.G18071' => 'tpr', 'TPR.G19055' => 'tpr', 'TPR.G19600' => 'tpr', 'TPR.G4184' => 'tpr', 'TWI12G0590' => 'twi', 'TWI18G1418' => 'twi', 'TWI36G0911' => 'twi', 'TWI36G1449' => 'twi', 'TWI38G2058' => 'twi', 'TWI39G0308' => 'twi', 'TWI63G0822' => 'twi', 'unitig_26.g9931' => 'ugi', 'unitig_37.g12582' => 'ugi', 'unitig_46.g18330' => 'ugi', 'unitig_52.g17336' => 'ugi', 'unitig_62.g23193' => 'ugi', 'unitig_746.g26653' => 'ugi', 'unitig_749.g13947' => 'ugi', 'VMungo0540G0269' => 'vmu', 'VMungo0647G0217' => 'vmu', 'VMungo1080G0467' => 'vmu', 'VMungo1127G0150' => 'vmu', 'VMungo1127G1677' => 'vmu', 'Zm00001eb171840' => 'zma', 'Zm00001eb233530' => 'zma', 'Zm00001eb281310' => 'zma', 'Zm00001eb389190' => 'zma', 'Zm00001eb413010' => 'zma' ) $gf_id = 'HOM05D001117' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001117' ) $data_identifier = 'HOM05D001117' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'ach' => (int) 7, 'amhyb' => (int) 14, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 3, 'bca' => (int) 22, 'bol' => (int) 9, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 4, 'chi' => (int) 5, 'cru' => (int) 6, 'car' => (int) 2, 'ccan' => (int) 4, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 4, 'cil' => (int) 8, 'cla' => (int) 5, 'col' => (int) 5, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 11, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 18, 'fve' => (int) 5, 'gma' => (int) 12, 'ghi' => (int) 17, 'gra' => (int) 8, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 6, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 1, 'lal' => (int) 11, 'lonja' => (int) 2, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 8, 'mpo' => (int) 2, 'mbi' => (int) 6, 'mdo' => (int) 3, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 5, 'ama' => (int) 6, 'nta' => (int) 14, 'nnu' => (int) 3, 'oeu' => (int) 10, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 11, 'ppa' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 3, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 5, 'rsi' => (int) 6, 'sbr' => (int) 10, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 6, 'sgi' => (int) 1, 'sas' => (int) 7, 'smo' => (int) 1, 'sly' => (int) 6, 'spe' => (int) 6, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 5, 'twi' => (int) 7, 'ugi' => (int) 7, 'vmu' => (int) 5, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb413010' $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